Chapter 5 Alpha diversity

5.1 Filtered

#Calculate Hill numbers
richness <- genome_counts_filt %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=0) %>%
            t() %>%
            as.data.frame() %>%
            rename(richness=1) %>%
            rownames_to_column(var="microsample")

neutral <- genome_counts_filt %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=1) %>%
            t() %>%
            as.data.frame() %>%
            rename(neutral=1) %>%
            rownames_to_column(var="microsample")

phylogenetic <- genome_counts_filt %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=1,tree=genome_tree) %>%
            t() %>%
            as.data.frame() %>%
            rename(phylogenetic=1) %>%
            rownames_to_column(var="microsample")

# Merge alpha diversities
alpha_diversity <- richness %>%
      full_join(neutral,by=join_by(microsample==microsample)) %>%
      full_join(phylogenetic,by=join_by(microsample==microsample)) %>%
      left_join(sample_metadata, by=join_by(microsample==microsample))

# Write alpha diversities
alpha_diversity %>% write_tsv("results/alpha_div_filtered.tsv")

# Print alpha diversity
alpha_diversity %>%
  select(microsample,richness, neutral, phylogenetic, section, buffer, batch, protocol, Xcoord, Ycoord, size) %>%
  tt()
tinytable_3wl4v01hew03pqzahdch
microsample richness neutral phylogenetic section buffer batch protocol Xcoord Ycoord size
M300554 105 45.801912 3.911416 Caecum right B11 MSEB0006 full_ulv2 74953.325 27445.67 4976
M300555 3 2.654441 1.657236 Caecum right B11 MSEB0006 full_ulv2 72020.280 33695.14 4976
M300556 3 2.921247 1.813378 Caecum right B11 MSEB0006 full_ulv2 75415.387 27819.35 4976
M300557 81 43.169579 3.712575 Caecum right B11 MSEB0006 full_ulv2 76113.477 28351.85 4976
M300559 105 46.235275 3.924148 Caecum right B11 MSEB0006 full_ulv2 76849.228 29025.05 4976
M300560 99 44.437305 4.065477 Caecum right B11 MSEB0006 full_ulv2 75971.705 29352.86 4976
M300561 103 44.311493 4.092159 Caecum right B11 MSEB0006 full_ulv2 76680.937 29558.16 4976
M300562 103 46.882732 4.021131 Caecum right B11 MSEB0006 full_ulv2 74883.318 29170.18 5140
M300563 109 47.059960 3.989914 Caecum right B11 MSEB0006 full_ulv2 75220.992 29120.51 5140
M300564 12 10.477468 2.957506 Caecum right B11 MSEB0006 full_ulv2 75894.617 29134.86 5140
M300566 93 43.059847 3.761573 Caecum right B11 MSEB0006 full_ulv2 76922.541 29224.45 5140
M300567 99 44.029116 4.012374 Caecum right B11 MSEB0006 full_ulv2 77492.203 29097.78 5140
M300569 100 46.805777 4.101282 Caecum right B11 MSEB0006 full_ulv2 77495.465 28977.76 5140
M300570 100 44.462204 3.951953 Caecum right B11 MSEB0006 full_ulv2 74950.841 28473.11 4815
M300571 94 42.482781 3.877417 Caecum right B11 MSEB0006 full_ulv2 75619.946 28632.40 4815
M300572 56 32.680577 3.739918 Caecum right B11 MSEB0006 full_ulv2 76345.933 29031.81 4815
M300574 97 43.914978 3.965100 Caecum right B11 MSEB0006 full_ulv2 76920.997 29347.99 4815
M300576 92 43.158898 3.953223 Caecum right B11 MSEB0006 full_ulv2 77104.532 29588.79 4815
M300577 103 44.666492 3.976265 Caecum right B11 MSEB0006 full_ulv2 77418.895 29907.92 4815
M300578 101 44.526067 3.915702 Caecum right B12 MSEB0006 full_ulv2 76897.212 30198.48 5140
M300580 102 43.777961 3.939951 Caecum right B12 MSEB0006 full_ulv2 77026.940 30039.53 5140
M300581 79 39.975639 3.872346 Caecum right B12 MSEB0006 full_ulv2 77028.597 29718.20 5140
M300582 78 38.898531 3.881888 Caecum right B12 MSEB0006 full_ulv2 77019.213 29448.24 5140
M300583 95 38.373844 3.975637 Caecum right B12 MSEB0006 full_ulv2 77009.202 28923.10 5140
M300584 104 44.918626 3.965482 Caecum right B12 MSEB0006 full_ulv2 77019.413 28061.84 5140
M300588 102 42.618728 3.970993 Caecum right B12 MSEB0006 full_ulv2 75330.017 26890.36 5141
M300589 99 41.459691 3.936518 Caecum right B12 MSEB0006 full_ulv2 75862.866 27323.96 5141
M300590 96 40.482162 4.103071 Caecum right B12 MSEB0006 full_ulv2 76508.231 27653.84 5141
M300592 103 40.971234 4.064549 Caecum right B12 MSEB0006 full_ulv2 77351.464 28017.27 5141
M300593 98 42.126550 4.054750 Caecum right B12 MSEB0006 full_ulv2 77854.216 28261.49 5141
M300594 96 43.659879 4.039384 Caecum right B12 MSEB0006 full_ulv2 75509.650 26477.82 4976
M300595 102 37.738766 4.048987 Caecum right B12 MSEB0006 full_ulv2 75650.540 26591.91 4976
M300596 105 40.160724 4.033115 Caecum right B12 MSEB0006 full_ulv2 75822.838 26598.11 4976
M300597 100 40.582505 4.079831 Caecum right B12 MSEB0006 full_ulv2 76147.102 26625.28 4976
M300598 101 41.887011 4.025419 Caecum right B12 MSEB0006 full_ulv2 76899.245 26623.52 4976
M300599 104 42.932100 3.943969 Caecum right B12 MSEB0006 full_ulv2 76852.725 26643.02 4976
M300602 4 3.258694 1.446601 Ileum B11 MSEB0006 full_ulv2 104424.700 42749.48 5140
M300603 3 2.026603 1.264579 Ileum B11 MSEB0006 full_ulv2 104606.900 42459.54 5140
M300605 2 1.729081 1.214454 Ileum B11 MSEB0006 full_ulv2 104954.500 42730.89 5140
M300606 1 1.000000 1.000000 Ileum B11 MSEB0006 full_ulv2 105122.500 42666.74 5140
M300608 4 2.614424 1.427086 Ileum B11 MSEB0006 full_ulv2 105262.700 42589.77 5140
M300609 4 3.096111 1.455646 Ileum B11 MSEB0006 full_ulv2 105328.900 42703.60 5140
M300610 4 3.092445 1.478474 Ileum B11 MSEB0006 full_ulv2 105102.400 41497.10 4976
M300611 1 1.000000 1.000000 Ileum B11 MSEB0006 full_ulv2 105146.000 41596.22 4976
M300612 4 3.200070 1.466971 Ileum B11 MSEB0006 full_ulv2 105281.000 41702.52 4976
M300613 1 1.000000 1.000000 Ileum B11 MSEB0006 full_ulv2 105408.300 41533.66 4976
M300616 3 1.602470 1.192713 Ileum B11 MSEB0006 full_ulv2 105595.700 41999.37 4976
M300617 4 2.597621 1.410566 Ileum B11 MSEB0006 full_ulv2 105983.000 42106.21 4976
M300619 3 1.859573 1.237721 Ileum B11 MSEB0006 full_ulv2 106845.700 41525.80 5306
M300622 3 2.658765 1.353273 Ileum B11 MSEB0006 full_ulv2 107262.300 42133.87 5306
M300623 3 2.873136 1.380176 Ileum B11 MSEB0006 full_ulv2 107820.600 41925.02 5306
M300624 1 1.000000 1.000000 Ileum B11 MSEB0006 full_ulv2 107233.500 41764.35 5306
M300627 3 2.862931 1.378919 Ileum B12 MSEB0006 full_ulv2 108112.000 45420.81 4815
M300628 4 2.628829 1.499791 Ileum B12 MSEB0006 full_ulv2 108221.600 45346.45 4815
M300629 4 1.907144 1.302185 Ileum B12 MSEB0006 full_ulv2 108085.500 45636.13 4815
M300630 4 1.854313 1.280920 Ileum B12 MSEB0006 full_ulv2 108093.700 45848.93 4815
M300631 5 3.608828 1.721713 Ileum B12 MSEB0006 full_ulv2 107697.500 45704.29 4815
M300633 6 2.179216 1.433128 Ileum B12 MSEB0006 full_ulv2 107727.500 45487.09 4815
M300634 5 2.654260 1.433183 Ileum B12 MSEB0006 full_ulv2 106635.900 42106.55 5384
M300636 4 2.513021 1.484550 Ileum B12 MSEB0006 full_ulv2 106545.500 42220.70 5384
M300638 4 2.712719 1.464181 Ileum B12 MSEB0006 full_ulv2 106647.000 42288.86 5384
M300639 7 2.562594 1.486765 Ileum B12 MSEB0006 full_ulv2 106800.500 41821.88 5384
M300640 3 2.025162 1.264308 Ileum B12 MSEB0006 full_ulv2 107052.700 42525.49 5384
M300642 1 1.000000 1.000000 Ileum B12 MSEB0006 full_ulv2 108030.700 43599.50 4976
M300644 5 1.600004 1.208205 Ileum B12 MSEB0006 full_ulv2 NA NA NA
M300645 5 1.502894 1.239684 Ileum B12 MSEB0006 full_ulv2 107988.200 43509.47 4976
M300647 5 3.154388 1.457167 Ileum B12 MSEB0006 full_ulv2 107969.500 43138.84 4976
M300648 5 1.758864 1.265810 Ileum B12 MSEB0006 full_ulv2 107883.700 43169.50 4976
M300651 102 46.742684 3.929222 Caecum right B12 MSEB0009 full_celero 11906.706 17302.78 5140
M300652 100 42.923634 4.114776 Caecum right B12 MSEB0009 full_celero 14050.460 17001.92 5140
M300654 96 37.251363 3.830623 Caecum right B12 MSEB0009 full_celero 14807.470 19475.98 5140
M300656 7 6.275011 2.411725 Caecum right B12 MSEB0009 full_celero 15095.242 18655.46 5140
M300657 34 19.736256 3.557363 Caecum right B12 MSEB0009 full_celero 15154.326 19081.92 5140
M300658 99 42.314901 4.036385 Caecum right B12 MSEB0009 full_celero 9192.814 19234.39 4976
M300659 119 42.309365 3.994236 Caecum right B12 MSEB0009 full_celero 12511.076 19365.33 4976
M300661 103 39.608207 3.905772 Caecum right B12 MSEB0009 full_celero 11699.514 20259.00 4976
M300662 104 44.515529 3.819290 Caecum right B12 MSEB0009 full_celero 13804.910 20094.72 4976
M300664 15 11.273184 3.132174 Caecum right B12 MSEB0009 full_celero 12513.988 21896.24 4976
M300665 4 2.814786 1.704808 Caecum right B12 MSEB0009 full_celero 9669.578 19330.82 4976
M300666 111 42.796930 3.995646 Caecum right B12 MSEB0009 full_celero 10924.656 21602.49 5384
M300668 108 39.784202 3.977135 Caecum right B12 MSEB0009 full_celero 14208.788 22187.84 5384
M300669 104 41.185041 4.089677 Caecum right B12 MSEB0009 full_celero 13658.990 21278.18 5384
M300670 85 39.361771 3.851039 Caecum right B12 MSEB0009 full_celero 15752.910 20908.01 5384
M300671 104 40.283873 4.066253 Caecum right B12 MSEB0009 full_celero 13086.410 21703.25 5384
M300672 94 40.061994 3.858419 Caecum right B12 MSEB0009 full_celero 13311.294 20916.06 5384
M300673 98 38.528300 4.029266 Caecum right B12 MSEB0009 full_celero 14520.766 22307.33 5384
M300674 109 44.864962 3.943580 Caecum right B12 MSEB0009 full_celero 12054.270 23154.78 5051
M300675 114 44.861236 3.939224 Caecum right B12 MSEB0009 full_celero 13501.846 20960.88 5051
M300676 96 39.189195 4.028682 Caecum right B12 MSEB0009 full_celero 14952.726 23717.40 5051
M300677 31 20.289760 3.183021 Caecum right B12 MSEB0009 full_celero 12773.380 21535.84 5051
M300678 116 43.357715 3.994201 Caecum right B12 MSEB0009 full_celero 12504.528 21793.47 5051
M300679 104 41.578976 3.992278 Caecum right B12 MSEB0009 full_celero 12589.016 20536.83 5051
M300680 112 44.937212 4.032103 Caecum right B12 MSEB0009 full_celero 13215.834 22405.85 5051
M300681 2 1.999637 1.764608 Caecum right B12 MSEB0009 full_celero NA NA NA
M300682 6 5.048966 2.842439 Caecum right B12 MSEB0009 half_ulv2 14464.852 18168.78 4976
M300683 96 39.991157 4.070488 Caecum right B12 MSEB0009 half_ulv2 15660.538 17029.20 4976
M300684 97 38.327913 3.983029 Caecum right B12 MSEB0009 half_ulv2 13001.740 18200.66 4976
M300687 106 42.965867 3.998442 Caecum right B12 MSEB0009 half_ulv2 14317.052 18439.38 4976
M300688 102 41.106310 3.898127 Caecum right B12 MSEB0009 half_ulv2 14710.394 18826.57 4976
M300689 94 40.781853 4.001373 Caecum right B12 MSEB0009 half_ulv2 14280.268 17123.50 4976
M300690 97 40.763262 4.104831 Caecum right B12 MSEB0009 half_ulv2 9132.332 19004.86 5140
M300691 117 43.804454 4.019294 Caecum right B12 MSEB0009 half_ulv2 9914.940 18812.94 5140
M300692 105 44.986055 4.091548 Caecum right B12 MSEB0009 half_ulv2 12814.906 20311.48 5140
M300694 84 37.691549 3.890651 Caecum right B12 MSEB0009 half_ulv2 12365.162 19024.05 5140
M300695 97 42.198415 3.886696 Caecum right B12 MSEB0009 half_ulv2 13549.800 18825.93 5140
M300696 103 41.230141 4.023761 Caecum right B12 MSEB0009 half_ulv2 12894.764 18832.32 5140
M300697 88 40.517297 4.047342 Caecum right B12 MSEB0009 half_ulv2 13465.594 19185.00 5140
M300698 7 2.528667 1.440155 Ileum B02 MSEB0009 full_ulv2 NA NA NA
M300699 8 2.595056 1.452254 Ileum B02 MSEB0009 full_ulv2 NA NA NA
M300700 9 3.078360 1.535261 Ileum B12 MSEB0009 full_ulv2 NA NA NA
M300701 8 3.259559 1.578356 Ileum B12 MSEB0009 full_ulv2 NA NA NA
Undeter 114 45.506971 4.113590 NA NA NA NA NA NA NA 
# Print alpha diversity summary
alpha_diversity %>%
  select(richness, neutral, phylogenetic, section, batch, protocol) %>%
  group_by(section, batch, protocol) %>%
  summarise(richness=mean(richness), neutral=mean(neutral), phylogenetic=mean(phylogenetic)) %>%
  tt()
tinytable_cu0fpnau22l88wwxyskl
section batch protocol richness neutral phylogenetic
Caecum right MSEB0006 full_ulv2 89.50000 39.563947 3.814879
Caecum right MSEB0009 full_celero 83.50000 34.570989 3.660827
Caecum right MSEB0009 half_ulv2 91.69231 38.416403 3.912156
Ileum MSEB0006 full_ulv2 3.59375 2.222942 1.320274
Ileum MSEB0009 full_ulv2 8.00000 2.865410 1.501506
NA NA NA 114.00000 45.506971 4.113590 
alpha_diversity %>%
  pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,protocol,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
  left_join(quality,by=join_by(microsample==microsample)) %>%
  mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
  ggplot(aes(x=protocol, y=value, color=quality, group=protocol))+ 
        scale_color_gradient(low = "red", high = "green", name = "Quality") +
        geom_boxplot(outlier.shape = NA) +
        geom_jitter(width=0.2) + 
        facet_grid(metric ~ section, scales = "free")

alpha_diversity %>%
  pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,protocol,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
  left_join(quality,by=join_by(microsample==microsample)) %>%
  mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
  ggplot(aes(x=batch, y=value, color=quality, group=batch))+ 
        scale_color_gradient(low = "red", high = "green", name = "Quality") +
        geom_boxplot(outlier.shape = NA) +
        geom_jitter(width=0.2) + 
        facet_grid(metric ~ section, scales = "free")

5.2 Unfiltered

#Calculate Hill numbers
richness <- genome_counts %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=0) %>%
            t() %>%
            as.data.frame() %>%
            rename(richness=1) %>%
            rownames_to_column(var="microsample")

neutral <- genome_counts %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=1) %>%
            t() %>%
            as.data.frame() %>%
            rename(neutral=1) %>%
            rownames_to_column(var="microsample")

phylogenetic <- genome_counts %>%
            column_to_rownames(var="genome") %>%
            select(where(~!all(. == 0))) %>%
            hilldiv(.,q=1,tree=genome_tree) %>%
            t() %>%
            as.data.frame() %>%
            rename(phylogenetic=1) %>%
            rownames_to_column(var="microsample")

# Merge alpha diversities
alpha_diversity <- richness %>%
      full_join(neutral,by=join_by(microsample==microsample)) %>%
      full_join(phylogenetic,by=join_by(microsample==microsample)) %>%
      left_join(sample_metadata, by=join_by(microsample==microsample))

# Write alpha diversities
alpha_diversity %>% write_tsv("results/alpha_div_unfiltered.tsv")

# Print alpha diversity
alpha_diversity %>%
  select(microsample,richness, neutral, phylogenetic, section, buffer, Xcoord, Ycoord, size) %>%
  tt()
tinytable_ezyuru4h8o4dt42rvvfy
microsample richness neutral phylogenetic section buffer Xcoord Ycoord size
M300554 252 59.048724 4.005426 Caecum right B11 74953.325 27445.67 4976
M300555 234 29.591689 3.136402 Caecum right B11 72020.280 33695.14 4976
M300556 242 52.377341 3.862228 Caecum right B11 75415.387 27819.35 4976
M300557 252 60.880377 3.919625 Caecum right B11 76113.477 28351.85 4976
M300558 147 16.388623 3.084364 Caecum right B11 NA NA NA
M300559 252 59.602278 4.019172 Caecum right B11 76849.228 29025.05 4976
M300560 252 58.645287 4.181971 Caecum right B11 75971.705 29352.86 4976
M300561 252 57.105278 4.190661 Caecum right B11 76680.937 29558.16 4976
M300562 252 60.378741 4.115130 Caecum right B11 74883.318 29170.18 5140
M300563 252 59.645294 4.072592 Caecum right B11 75220.992 29120.51 5140
M300564 246 52.890970 4.203353 Caecum right B11 75894.617 29134.86 5140
M300565 48 13.113524 4.215440 Caecum right B11 72986.812 36482.20 5140
M300566 251 58.164898 3.882696 Caecum right B11 76922.541 29224.45 5140
M300567 252 57.810869 4.124295 Caecum right B11 77492.203 29097.78 5140
M300568 40 10.638020 2.635867 Caecum right B11 NA NA NA
M300569 252 60.745119 4.196834 Caecum right B11 77495.465 28977.76 5140
M300570 252 57.723816 4.052962 Caecum right B11 74950.841 28473.11 4815
M300571 251 56.661744 4.017740 Caecum right B11 75619.946 28632.40 4815
M300572 249 56.949762 4.191364 Caecum right B11 76345.933 29031.81 4815
M300573 178 34.564442 3.598634 Caecum right B11 74609.411 34469.39 4815
M300574 251 57.725467 4.082745 Caecum right B11 76920.997 29347.99 4815
M300575 135 59.863456 4.655632 Caecum right B11 NA NA NA
M300576 251 57.389815 4.083745 Caecum right B11 77104.532 29588.79 4815
M300577 252 57.842513 4.079376 Caecum right B11 77418.895 29907.92 4815
M300578 252 57.743125 4.012410 Caecum right B12 76897.212 30198.48 5140
M300579 221 38.829262 3.357156 Caecum right B12 73304.285 36352.33 5140
M300580 250 55.871239 4.042301 Caecum right B12 77026.940 30039.53 5140
M300581 252 56.693254 4.077549 Caecum right B12 77028.597 29718.20 5140
M300582 251 55.908533 4.078589 Caecum right B12 77019.213 29448.24 5140
M300583 252 51.029088 4.100996 Caecum right B12 77009.202 28923.10 5140
M300584 252 57.684739 4.058398 Caecum right B12 77019.413 28061.84 5140
M300585 85 36.312174 5.379855 Caecum right B12 NA NA NA
M300586 48 21.091967 4.510739 Caecum right B12 73652.539 35857.69 5141
M300587 8 3.491849 1.592392 Caecum right B12 NA NA NA
M300588 252 54.764773 4.072549 Caecum right B12 75330.017 26890.36 5141
M300589 253 54.565428 4.052600 Caecum right B12 75862.866 27323.96 5141
M300590 252 53.695112 4.232105 Caecum right B12 76508.231 27653.84 5141
M300591 193 44.669792 3.308027 Caecum right B12 76848.926 27815.44 5141
M300592 251 52.703789 4.157326 Caecum right B12 77351.464 28017.27 5141
M300593 253 54.697582 4.159239 Caecum right B12 77854.216 28261.49 5141
M300594 252 57.267685 4.154592 Caecum right B12 75509.650 26477.82 4976
M300595 251 49.303188 4.159722 Caecum right B12 75650.540 26591.91 4976
M300596 252 51.537550 4.129928 Caecum right B12 75822.838 26598.11 4976
M300597 251 52.894386 4.187497 Caecum right B12 76147.102 26625.28 4976
M300598 252 54.366506 4.127848 Caecum right B12 76899.245 26623.52 4976
M300599 252 55.014439 4.041644 Caecum right B12 76852.725 26643.02 4976
M300600 37 12.471508 3.871589 Caecum right B12 NA NA NA
M300601 122 44.752920 6.549661 Caecum right B12 72982.582 21722.53 4976
M300602 195 3.770399 1.526286 Ileum B11 104424.700 42749.48 5140
M300603 172 3.443781 1.761321 Ileum B11 104606.900 42459.54 5140
M300604 54 11.488595 3.430860 Ileum B11 101758.400 36668.70 5140
M300605 154 3.468041 1.580848 Ileum B11 104954.500 42730.89 5140
M300606 231 42.312840 4.055184 Ileum B11 105122.500 42666.74 5140
M300607 25 4.742713 1.877699 Ileum B11 NA NA NA
M300608 180 3.093547 1.514223 Ileum B11 105262.700 42589.77 5140
M300609 207 3.586403 1.515176 Ileum B11 105328.900 42703.60 5140
M300610 193 3.434464 1.521143 Ileum B11 105102.400 41497.10 4976
M300611 75 4.120703 1.781889 Ileum B11 105146.000 41596.22 4976
M300612 186 3.576177 1.512044 Ileum B11 105281.000 41702.52 4976
M300613 71 2.227148 1.360170 Ileum B11 105408.300 41533.66 4976
M300614 51 13.957408 4.473484 Ileum B11 101928.600 37181.60 4976
M300615 76 33.344988 4.963147 Ileum B11 NA NA NA
M300616 174 1.845652 1.249203 Ileum B11 105595.700 41999.37 4976
M300617 236 5.332503 1.984855 Ileum B11 105983.000 42106.21 4976
M300618 56 8.503252 2.626672 Ileum B11 101861.400 37375.71 5306
M300619 175 2.550470 1.410755 Ileum B11 106845.700 41525.80 5306
M300620 28 7.640770 2.905044 Ileum B11 NA NA NA
M300621 119 12.148781 3.349201 Ileum B11 107360.500 41744.06 5306
M300622 221 4.591257 1.766175 Ileum B11 107262.300 42133.87 5306
M300623 160 3.966379 1.799967 Ileum B11 107820.600 41925.02 5306
M300624 115 1.651694 1.232074 Ileum B11 107233.500 41764.35 5306
M300625 144 5.388601 2.320102 Ileum B11 107258.100 42448.02 5306
M300626 41 8.538645 2.863586 Ileum B12 NA NA NA
M300627 144 3.518088 1.512361 Ileum B12 108112.000 45420.81 4815
M300628 175 3.173885 1.607903 Ileum B12 108221.600 45346.45 4815
M300629 182 2.393480 1.450458 Ileum B12 108085.500 45636.13 4815
M300630 182 2.332205 1.406259 Ileum B12 108093.700 45848.93 4815
M300631 208 4.627633 1.966486 Ileum B12 107697.500 45704.29 4815
M300632 139 31.364862 4.012416 Ileum B12 102872.400 38456.93 4815
M300633 216 2.511084 1.495177 Ileum B12 107727.500 45487.09 4815
M300634 213 3.122181 1.540972 Ileum B12 106635.900 42106.55 5384
M300635 30 5.405679 2.215422 Ileum B12 NA NA NA
M300636 204 3.509144 1.743930 Ileum B12 106545.500 42220.70 5384
M300637 51 2.910588 1.509677 Ileum B12 106948.100 42956.50 5384
M300638 203 3.460643 1.642359 Ileum B12 106647.000 42288.86 5384
M300639 224 2.990724 1.567194 Ileum B12 106800.500 41821.88 5384
M300640 139 2.600750 1.476414 Ileum B12 107052.700 42525.49 5384
M300641 98 27.021534 5.575144 Ileum B12 103203.400 38334.96 5384
M300642 72 2.706444 1.584137 Ileum B12 108030.700 43599.50 4976
M300643 16 5.123028 1.769523 Ileum B12 101876.900 39000.58 4976
M300644 225 1.815382 1.244790 Ileum B12 NA NA NA
M300645 192 1.687109 1.278009 Ileum B12 107988.200 43509.47 4976
M300646 64 13.841432 3.496467 Ileum B12 NA NA NA
M300647 201 3.557171 1.509236 Ileum B12 107969.500 43138.84 4976
M300648 198 2.029309 1.315127 Ileum B12 107883.700 43169.50 4976
M300649 74 4.148091 1.828161 Ileum B12 107984.200 43047.52 4976
M300650 90 25.547686 5.490960 Caecum right B12 13017.480 NA NA
M300651 252 60.334462 4.037827 Caecum right B12 11906.706 17302.78 5140
M300652 252 55.706583 4.230868 Caecum right B12 14050.460 17001.92 5140
M300653 205 23.115889 2.885944 Caecum right B12 15132.646 18629.72 5140
M300654 252 49.719436 3.958627 Caecum right B12 14807.470 19475.98 5140
M300655 66 11.835013 3.758529 Caecum right B12 12921.636 17630.90 5140
M300656 237 51.627998 3.879326 Caecum right B12 15095.242 18655.46 5140
M300657 249 40.393213 4.019623 Caecum right B12 15154.326 19081.92 5140
M300658 252 55.646080 4.151520 Caecum right B12 9192.814 19234.39 4976
M300659 252 52.072344 4.069240 Caecum right B12 12511.076 19365.33 4976
M300660 76 5.499699 2.285934 Caecum right B12 11930.670 19818.58 4976
M300661 253 51.583910 4.013095 Caecum right B12 11699.514 20259.00 4976
M300662 251 56.603450 3.916391 Caecum right B12 13804.910 20094.72 4976
M300663 97 10.308725 4.266069 Caecum right B12 NA NA NA
M300664 249 30.493582 3.840296 Caecum right B12 12513.988 21896.24 4976
M300665 240 19.254617 3.317076 Caecum right B12 9669.578 19330.82 4976
M300666 252 53.743891 4.080995 Caecum right B12 10924.656 21602.49 5384
M300667 73 21.078963 5.788265 Caecum right B12 NA NA NA
M300668 252 50.277071 4.072904 Caecum right B12 14208.788 22187.84 5384
M300669 252 52.995755 4.195787 Caecum right B12 13658.990 21278.18 5384
M300670 249 54.520367 4.020114 Caecum right B12 15752.910 20908.01 5384
M300671 251 52.121850 4.170802 Caecum right B12 13086.410 21703.25 5384
M300672 252 53.386952 3.983508 Caecum right B12 13311.294 20916.06 5384
M300673 251 50.112142 4.146929 Caecum right B12 14520.766 22307.33 5384
M300674 252 56.789427 4.028199 Caecum right B12 12054.270 23154.78 5051
M300675 252 55.626538 4.026539 Caecum right B12 13501.846 20960.88 5051
M300676 250 52.022526 4.150433 Caecum right B12 14952.726 23717.40 5051
M300677 247 51.570297 3.979858 Caecum right B12 12773.380 21535.84 5051
M300678 253 53.265316 4.073765 Caecum right B12 12504.528 21793.47 5051
M300679 252 52.843053 4.090399 Caecum right B12 12589.016 20536.83 5051
M300680 252 56.085699 4.115161 Caecum right B12 13215.834 22405.85 5051
M300681 199 15.133302 3.203389 Caecum right B12 NA NA NA
M300682 237 49.016763 4.129097 Caecum right B12 14464.852 18168.78 4976
M300683 252 52.766786 4.190538 Caecum right B12 15660.538 17029.20 4976
M300684 251 49.976106 4.087444 Caecum right B12 13001.740 18200.66 4976
M300685 222 32.549462 4.768086 Caecum right B12 NA NA NA
M300686 215 58.246778 3.986024 Caecum right B12 14173.260 17741.15 4976
M300687 251 54.586232 4.091225 Caecum right B12 14317.052 18439.38 4976
M300688 251 53.413916 4.010619 Caecum right B12 14710.394 18826.57 4976
M300689 252 54.070423 4.127761 Caecum right B12 14280.268 17123.50 4976
M300690 252 53.782859 4.233271 Caecum right B12 9132.332 19004.86 5140
M300691 252 54.125918 4.099929 Caecum right B12 9914.940 18812.94 5140
M300692 252 57.228981 4.188129 Caecum right B12 12814.906 20311.48 5140
M300693 58 23.416149 5.412036 Caecum right B12 NA NA NA
M300694 251 51.989711 4.068597 Caecum right B12 12365.162 19024.05 5140
M300695 252 55.251650 4.033557 Caecum right B12 13549.800 18825.93 5140
M300696 251 53.015006 4.124372 Caecum right B12 12894.764 18832.32 5140
M300697 252 55.034448 4.188927 Caecum right B12 13465.594 19185.00 5140
M300698 239 2.871161 1.498583 Ileum B02 NA NA NA
M300699 240 2.908721 1.497934 Ileum B02 NA NA NA
M300700 244 3.598605 1.600967 Ileum B12 NA NA NA
M300701 243 3.910067 1.663592 Ileum B12 NA NA NA
M300702 8 3.007004 1.354425 Caecum right NA NA NA NA
M300703 6 2.681496 1.290717 Caecum right NA NA NA NA
Undeter 253 56.603367 4.191806 NA NA NA NA NA 
# Print alpha diversity summary
alpha_diversity %>%
  select(richness, neutral, phylogenetic, section, buffer) %>%
  group_by(section, buffer) %>%
  summarise(richness=mean(richness), neutral=mean(neutral), phylogenetic=mean(phylogenetic)) %>%
  tt()
tinytable_ulojsdrcy59t2x94oiw6
section buffer richness neutral phylogenetic
Caecum right B11 220.6250 50.239502 3.942011
Caecum right B12 219.5417 46.071485 4.088926
Caecum right NA 7.0000 2.844250 1.322571
Ileum B02 239.5000 2.889941 1.498259
Ileum B11 137.4167 7.924440 2.229897
Ileum B12 153.0000 5.842222 1.956760
NA NA 253.0000 56.603367 4.191806 
alpha_diversity %>%
  pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,protocol,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
  left_join(quality,by=join_by(microsample==microsample)) %>%
  mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
  ggplot(aes(x=protocol, y=value, color=quality, group=protocol))+ 
        scale_color_gradient(low = "red", high = "green", name = "Quality") +
        geom_boxplot(outlier.shape = NA) +
        geom_jitter(width=0.2) + 
        facet_grid(metric ~ section, scales = "free")

alpha_diversity %>%
  pivot_longer(!c(microsample,section,cryosection,type,buffer,batch,protocol,Xcoord,Ycoord,size), names_to = "metric", values_to = "value") %>%
  left_join(quality,by=join_by(microsample==microsample)) %>%
  mutate(metric=factor(metric,levels=c("richness","neutral","phylogenetic"))) %>%
  ggplot(aes(x=batch, y=value, color=quality, group=batch))+ 
        scale_color_gradient(low = "red", high = "green", name = "Quality") +
        geom_boxplot(outlier.shape = NA) +
        geom_jitter(width=0.2) + 
        facet_grid(metric ~ section, scales = "free")